Metal transport across biomembranes: emerging models for a distinct chemistry

Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.     

Molecular simulations of phosphonium-based ionic liquid

Compared with imidazolium-based ionic liquids (ILs), phosphonium-based ILs have been proven to be more stable in thermodynamics and less expensive to manufacture. In this work, a kind of phosphonium-based IL, [PC₆C₆C₆C₁₄][Tf₂N], was studied under several conditions using molecular dynamics simulations based on both the all-atom force field (AAFF) and the united-atom force field. Liquid density was calculated to validate the force field. Compared with experimental data, good agreement was obtained for the simulated density based on the AAFF. Heat capacities at constant pressure were calculated at several temperatures, and good linear relationships were observed. Self-diffusion coefficients, viscosities and conductivities were also calculated to study the dynamics properties of this IL. The viscosity of this IL at 293 K was also compared with experimental data, and the error was in a reasonable range. In order to depict the microstructures of the IL, centre-of-mass and site-to-site radial distribution functions were employed. In addition, spatial distribution functions were investigated to present the more intuitive features.     

Predicting Liquid–Vapour Equilibria for Water Using an ab-initio Potential from Histogram Reweighting Monte Carlo Simulations

Abstract

The coexisting densities for an ab-initio model for water have been calculated using grand canonical Monte Carlo simulations with the histogram reweighting technique. Although good agreement with experimental data is found for the radial distribution function at room temperature, the predicted critical density and temperature are well below both the experimental value as well as predictions from semi-empirical potentials. Improvement in the repulsive part of the ab-initio potential is suggested as a way to obtain better agreement with experiment.     

Transportation behavior of alkali ions through a cell membrane ion channel. A quantum chemical description of a simplified isolated model

Quantum chemical model calculations were carried out for modeling the ion transport through an isolated ion channel of a cell membrane. An isolated part of a natural ion channel was modeled. The model channel was a calixarene derivative, hydrated sodium and potassium ions were the models of the transported ion. The electrostatic potential of the channel and the energy of the channel-ion system were calculated as a function of the alkali ion position. Both attractive and repulsive ion-channel interactions were found. The calculations - namely the dependence of the system energy and the atomic charges of the water molecules with respect to the position of the alkali ion in the channel - revealed the molecular-structural background of the potassium selectivity of this artificial ion channel. It was concluded that the studied ion channel mimics real biological ion channel quite well.     

Molecular Dynamics Simulations of Zinc Ions in Water Using CHARMM

Molecular Dynamics simulations of a zinc ion with 123 and 525 TIP3P-water molecules were carried out with CHARMM using two different Lennard-Jones parameter sets for the Zn²⁺ ion. The results were compared to published experimental and simulation data. Good agreement was found for radial distribution functions, number of hydrogen bonds, and diffusion coefficients. Experimental radial distribution functions were better reproduced by the original CHARMM22 parameter set than by the parameter set modified by Stote and Karplus. Diffusion coefficients were found to depend on the system size rather than on the parameter set used and were better reproduced by the larger systems. The divalent zinc ion exerts a strong influence on its hydration shell as indicated by the high first peak of the radial distribution function. Water molecules in the vicinity of the zinc ion show a slight deformation of the O-H bond length and of the H-O-H bond angle as compared to pure water. No water molecules from the first hydration shell were exchanged during 1 ns of MD simulation.Electronic Supplementary Material available.     

Ab Initio Molecular Dynamics for Simple Liquid Metals Based on the Hypernetted-Chain Approximation

Abstract

We present an ab initio molecular dynamics (MD) method for simple liquid metals based on the quantal hypernetted-chain (QHNC) theory derived from exact expressions for radial distribution functions (RDF's) of the electron-ion model for liquid metals. In our method based on the QHNC equations, the classical MD is performed repeatedly to determine a self-consistent effective interionic potential, which depends on the ion-ion RDF of the system. This resultant effective ionic potential is obtained to be consistent with the density distribution of a pseudoatom and the electron-ion RDF, as well as the ion-ion RDF and the ion-ion bridge function, which are determined exactly as a result of the repeated MD simulation. We have applied this QHNC-MD method for Li, Na, K, Rb, and Cs near the melting temperature using upto 16,000 particles for the MD simulation. It is found that the convergence of the effective interionic potential is fast enough for practical applications; typically two MD runs are enough for convergence of the effective ionic potential within accuracy of 3 to 4 digits. Furthermore the resultant static structure factor is in excellent agreement with experimental data of X-ray and/or neutron scatering.     

Recommended gas transport properties of argon at low density using ab initio potential

The most important transport properties of argon have been calculated using classical kinetic theory expressions in conjunction with high-quality ab initio potential energy values computed by Patkowski and Szalewicz. Dilute gas transport properties have been calculated for the viscosity, thermal conductivity, self-diffusion coefficient and thermal diffusion factor from 83 to 10,000 K. Comparisons between experimental transport property data and values presently calculated indicate that the present theoretical predictions may be employed as recommended values for this set of transport properties over a wide temperature range.     

A dosimetry method in the transverse plane of HDR Ir-192 brachytherapy source using gafchromic EBT2 film

Radiochromic film dosimetry is increasingly used in brachytherapy applications for its higher resolution ability as compared to other experimental methods. The present study was aimed to assess the accuracy and suitability of use of the improved radiochromic film model, Gafchromic EBT2, to evaluate the dose distribution in the transverse plane of microselectron HDR ¹⁹²Ir source.A specially designed and locally fabricated Polymethyl methacrylate (PMMA) phantom was used in this work for the experimental measurement of dose distribution around the source in its transverse plane. The AAPM TG-43U1 recommended radial dose function, g (r), and dose rate constant, Λ, for the source were measured using Gafchromic EBT2 film and thermoluminescent dosimeters (TLD). The EBT2 film measured dosimetric quantities were validated against their values obtained from the TLD measurements and previously published values for the same source available in literature.The dose rate constant and radial dose function for microselectron HDR ¹⁹²Ir source obtained from Gafchromic EBT2 film measurements are in agreement with their TLD measured results within 3.9% and 2.8% respectively. They also agree within the accepted range of uncertainty with their experimental and Monte Carlo calculated results reported in literature.This work demonstrates the suitability of using Gafchromic EBT2 film dosimetry in characterization of dose distribution in the transverse plane of HDR Ir-192 source. This is a more efficient method than TLD dosimetry at discrete and distant positions. Relative to TLD dosimetry, it is found to be better reproducible, easy to use and a less expensive method of dosimetry.     

Whole-tree water transport scales with sapwood capacitance in tropical forest canopy trees

The present study examines the manner in which several whole‐tree water transport properties scale with species‐specific variation in sapwood water storage capacity. The hypothesis that constraints on relationships between sapwood capacitance and other water relations characteristics lead to predictable scaling relationships between intrinsic capacitance and whole‐tree behaviour was investigated. Samples of sapwood from four tropical forest canopy tree species selected to represent a range of wood density, tree size and architecture, and taxonomic diversity were used to generate moisture release curves in thermocouple psychrometer chambers, from which species‐specific values of sapwood capacitance were calculated. Sapwood capacitance was then used to scale several whole‐tree water transport properties determined from measurements of upper branch and basal sap flow, branch water potential, and axial and radial movement of deuterated water (D₂O) injected into the base of the trunk as a tracer. Sapwood capacitance ranged from 83 to 416 kg m^?3 MPa^?1 among the four species studied and was strongly correlated with minimum branch water potential, soil‐to‐branch hydraulic conductance, daily utilization of stored water, and axial and radial movement of D₂O. The species‐independent scaling of several whole‐tree water transport properties with sapwood capacitance indicated that substantial convergence in plant function at multiple levels of biological organization was revealed by a simple variable related to a biophysical property of water transport tissue.     

Effect of cut-off distance used in molecular dynamics simulations on fluid properties

The effect of cut-off distance used in molecular dynamics (MD) simulations on fluid properties was studied systematically in both canonical (NVT) and isothermal–isobaric (NPT) ensembles. Results show that the cut-off distance in the NVT ensemble plays little role in determining the equilibrium structure of fluid if the ensemble has a high density. However, pressures calculated in the same NVT ensembles strongly depend on the cut-off distance used. In the NPT ensemble, cut-off distance plays a key role in determining fluid equilibrium structure, density and self-diffusion coefficient. The characteristic of the radial distribution function of fluid in NPT ensembles depending on the cut-off distance used in MD simulations means that the WCA theory (a perturbation theory developed by Weeks, Chandler and Andersen) is not suitable for NPT ensembles because the assumption (the effect of the attractive force in determining the liquid structure is negligible) used in the WCA theory is not valid. The dependence of fluid properties on the cut-off distance also indicates that using the WCA potential (the repulsive part of the intermolecular potential proposed in the WCA theory) to calculate fluid transport in heterogeneous systems could lead to significant errors or incorrect results.     

Molecular dynamics simulation of cross-linked urea-formaldehyde polymers for self-healing nanocomposites: prediction of mechanical properties and glass transition temperature

Urea-formaldehyde polymers, which are utilized in the adhesives industry, have recently been shown to be suitable materials for synthesizing micro/nanocapsules for use in self-healing (nano)composites. In this study, molecular dynamics was employed to simulate the process in which urea and formaldehyde are cross-linked via methylene and ether cross linkers, and to study the structure and mechanical/thermal properties of simulated poly(urea-formaldehyde)s (PUFs). The elastic stiffness constants of the simulated materials were calculated using the constant-strain (static) method. A temperature cycle was applied to the cross-linked PUFs, and the glass transition behavior of each material was investigated through the mean squared displacement (MSD) and temperature evolution of the energy and the specific volume of the polymer. The simulation results confirmed that there was considerable improvement in the properties of the poly(UF) materials upon cross linking. The radial distribution function was also used to study the local structures of the polymers, and this revealed that increasing the temperature and cross linking density results in a significant drop in hydrogen bonding intensity in the cross-linked PUF systems.     

Bioavailability of heavy metals in sediments of two coastal lagoons in Rio de Janeiro,Brazil

The distribution and bioavailability of trace metals in two contrasting tropical coastal lagoons were studied. The concentration of trace metals in aquatic macrophytes was compared with those found in sediments under weakly and strongly bound forms. The results showed that total metal concentrations in sediments did not explain the concentration found in plants. The highest concentrations in macrophytes were observed in the lagoon which had a higher fraction of metals weakly bound to sediments, but presented the lower total metal content. Low redox potential was the major variable keeping metals in non-bioavailable forms, possibly as refractory sulfides and metal-organic complexes. Among the macrophytes, rooted species showed lower concentrations of metals as compared to algae.     

DAPI binding to the DNA minor groove: a continuum solvent analysis

A continuum solvent model based on the generalized Born (GB) or finite-difference Poisson-Boltzmann (FDPB) approaches has been employed to compare the binding of 4'-6-diamidine-2-phenyl indole (DAPI) to the minor groove of various DNA sequences. Qualitative agreement between the results of GB and FDPB approaches as well as between calculated and experimentally observed trends regarding the sequence specificity of DAPI binding to B-DNA was obtained. Calculated binding energies were decomposed into various contributions to solvation and DNA-ligand interaction. DNA conformational adaptation was found to make a favorable contribution to the calculated total interaction energy but did not change the DAPI binding affinity ranking of different DNA sequences. The calculations indicate that closed complex formation is mainly driven by nonpolar contributions and was found to be disfavored electrostatically due to a desolvation penalty that outbalances the attractive Coulomb interaction. The calculated penalty was larger for DAPI binding to GC-rich sequences compared with AT-rich target sequences and generally larger for the FDPB vs the GB continuum model. A radial interaction profile for DAPI at different distances from the DNA minor groove revealed an electrostatic energy minimum a few Angstroms farther away from the closed binding geometry. The calculated electrostatic interaction up to this distance is attractive and it may stabilize a nonspecific binding arrangement.     

The molecular simulation of the miscibility,mechanical properties and physical cross-linking behavior of the poly(vinyl alcohol)/poly(acrylic acid) composited membranes

The miscibility and mechanical properties of poly vinyl alcohol (PVA) and poly acrylic acid (PAA)-composited membranes were studied with molecular simulation. The Flory–Huggins parameters (δ) were calculated to prove the good miscibility of PVA and PAA. The radial distribution functions of hydroxyl and carboxyl atoms and the average number of H-bonds were observed to indicate the degree of physical cross-linking between PVA and PAA. The influences of intermolecular physical cross-linking on the glass transition temperature and mechanical properties were estimated. The results revealed that the PVA/PAA membrane with a composition of 2:3 has the best plastic properties, which exhibits a good application value. All of the simulated results showed good agreement with the experimental data. It indicates that the method presented in this work has a promising application prospect.     

First- and second-approximation calculations in the relaxation function of high-sugar/polysaccharide systems

The distribution function of Maxwellian relaxation times (phi) was derived from the small- deformation dynamic properties of high-sugar/agarose, /deacylated gellan and /high-methoxy pectin mixtures. First-approximation calculations of phi employed the time derivative of the experimentally measured storage and viscous moduli, with the two traces converging at the theoretically predicted slope of - 0.5. Second-approximation calculations were based on phi, as derived by the first approximation, being a simple power function of relaxation times (tau(-m)). The slope m was measured at various points and used to derive correction factors for shifting the relaxation function to the second approximation. Thus, values of phi calculated from G' and G" were brought into satisfactory agreement, particularly in the recorded portion of the glass transition region. Once the function phi is accurately determined, it can be readily used for calculations of other viscoelastic properties.     

Phosphoinositides provide a regulatory mechanism of surface charge and active transport

Yeast cells, when grown in the presence of arsenate, are capable of accumulating phosphoinositides (PI) at the expense of inhibiting their degradation more than their synthesis. PI levels return to normal when the cells are cultured or exposed to media without arsenate. These reversible changes are employed as a tool to test the effect of inositide accumulation and dynamics on several membrane properties. In the PI-rich cells, phosphate and arsenate transport from low external concentrations (high affinity systems), as well as the transport of glycine, which enter the cells accompanied by protons, were increased. The proton ejection energized by glucose is also enhanced in the PI-rich cells that show a more efficient potassium inflow at pH 4.0-4.5. The membrane surface potential of the PI-rich cells was found to be 2-times higher than that of the normal cells, in agreement with the 2-fold increment in the PI. All the above mentioned alterations in membrane properties are reverted when the PI content of the PI-rich cells is reduced to the level of normal cells. The results show the participation of the phosphoinositides in the formation, maintenance and regulation of the membrane surface potential and their possible influence upon transport mechanisms.     

Electrostatic effects in proteins: comparison of dielectric and charge models.

Two approaches for calculating electrostatic effects in proteins are compared and ana analysis is presented of the dependence of calculated properties on the model used to define the charge distribution. Changes in electrostatic free energy have been calculated using a screened Coulomb potential (SCP) with a distance-dependent effective dielectric permittivity to model bulk solvent effects and a finite difference approach to solve the Poisson-Boltzmann (FDPB) equation. The properties calculated include shifts in dissociation constants of ionizable groups, the effect of annihilating surface charges on the binding of metals, and shifts in redox potentials due to changes in the charge of ionizable groups. In the proteins considered the charged sites are separated by 3.5-12 A. It is shown that for the systems studied in this distance range the SCP yields calculated values which are at least as accurate as those obtained from solution of the FDPB equation. In addition, in the distance range 3-5 A the SCP gives substantially better results than the FDPB equation. Possible sources of this difference between the two methods are discussed. Shifts in binding constants and redox potentials were calculated with several standard charge sets, and the resulting values show a variation of 20-40% between the 'best' and 'worst' cases. From this study it is concluded that in most applications, changes in electrostatic free energies can be calculated economically and reliably using an SCP approach with a single functional form of the screening function.     

The molecular mechanism and potential dependence of the Na+/glucose cotransporter.

Activity of the Na+/glucose cotransporter endogenously expressed in LLC-PK1 cells was measured using whole cell recording techniques under three different sodium concentration conditions: 1) externally saturating, zero trans; 2) 40 mM external, zero trans; and 3) externally saturating, 50 mM trans. Activity of the transporter with increasing concentrations of sugar was measured for each set of conditions, from which the maximal current for saturating sugar, Im, was determined. The Im measured shows substantial potential dependence for each set of conditions. The absolute Im and the relative potential dependence of Im compared among the various solute conditions were used to identify which loci in the transport cycle are responsible for potential-dependent changes in function. The experimental data were compared with the predicted Im values calculated from an eight-state, sequential, reversible model of a transport reaction kinetic scheme. Predictions derived from assignment of rate limitation and/or potential dependence to each of the 16 transitions in the transport pathway were derived and compared with the measured data. Most putative models were dismissed because of lack of agreement with the measured data, indicating that several steps along the transport pathway are not rate limiting and/or not potential dependent. Only two models were found that can completely account for the measured data. In one case, translocation of the free carrier must be rate limiting, and both extracellular sodium-binding events as well as translocation of both free and fully loaded carrier forms must be potential-dependent transitions. In the second case, translocation of the free carrier and dissociation of the first sodium to be released intracellularly must be equivalently rate limiting. In this case only the two translocation events are required to be potential dependent. The two external sodium-binding events might still be potential dependent, but this is not required to fit the data. Previous reports suggest that the first model is correct; however, no direct experimental data compel us to dismiss the second option as a feasible model.     

Dynamical Properties of Condensed Charged Polymer Melts

Abstract

Dynamical properties of condensed charged polymer melts are studied with a two-dimensional model and molecular dynamics simulation. Screened Coulombic interactions are assumed for the interactions between the monomer charges as well as the counterions which were introduced to neutralize the total monomer charges of polymer chains. Through molecular dynamics calculations, we have obtained the radial distribution function and velocity auto-correlation function, and their density dependences. As a structural characteristics in condensed charged polymer melts, we find that the monomers tend to form triangular structures locally. The radial distribution function for the center monomers implies that the polymer chains on our two-dimensional model are not entangled. The diffusion properties for both the counter-ions and innermost monomers are studied in detail. In this paper, we have also computed neutral polymer melts to study the effects of the presence of the long-range Coulombic interactions on the dynamical properties of polymer melts. We find that the Coulombic interactions significantly reduce the self diffusion. Snapshots analyses obtained from the molecular dynamics simulation suggest that the reptation model is not a proper model for two-dimensional polymer-chain melts, in which there are little entanglement effects in agreement with the result of the analyses for the radial distribution function.     

A simple model for the function of proteoglycans and collagen in the response to compression of the intervertebral disc.

The nucleus pulposus of the intervertebral disc exerts a pressure which enables it to support axial compression when contained by the annulus fibrosus. The disc was modelled as a thick-walled cylindrical pressure vessel in which the nucleus was contained radially by the annulus. As a result, the stress in the annulus had radial (compressive) as well as tangential (tensile) components. The radial stress at a given point in the annulus was considered to be balanced by the internal pressure which is expected to arise from the attraction of water by proteoglycans. There was a reasonable agreement between the calculated radial stress distribution and published results on the distribution of water within the annulus. As the internal pressure is expected to be isotropic, the annulus was expected to contribute to the axial resistance to compression of the disc; this contribution would be equal, in magnitude, to the radial stress. Predictions of the pressure distribution within the annulus were similar to published experimental measurements made in the radial and axial directions. The tangential stress within the annulus was considered to arise from the restoring stress in its strained collagen fibrils.